The 89-year-old monarch, who will become the country's longest serving sovereign in September, had in fact briefly attended London's King Edward VII Hospital for her annual health check-up, Buckingham Palace said.
"This was a routine, pre-scheduled appointment. The queen has now left the hospital," a spokeswoman said.
The palace statement came after a tweet by a BBC journalist Ahmen Khawaja implied Elizabeth had been rushed to the hospital for treatment.
The journalist later deleted the tweet and apologised for what she said was the result of a "silly prank".
The BBC said in a statement: "During a technical rehearsal for an obituary, tweets were mistakenly sent from the account of a BBC journalist saying that a member of the royal family had been taken ill. The tweets were swiftly deleted and we apologise for any offence."
The queen has cut back her public duties in recent years with heir-to-the-throne Prince Charles taking on more official roles. However, she attended parliament for its official state opening last week and has an engagement later on Wednesday at Buckingham Palace.
When she was hospitalised in March 2013 with symptoms of gastroenteritis, it was the first time she had needed hospital treatment in a decade.
(Reporting by Michael Holden; editing by Stephen Addison)
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